is this Workflow for texture atlas ok?
The bullet-proof method of using the Texture Atlas add-on works (at least for me) as follows: 


UV-unwrap and texture every object. 
Select all the objects you want to create the Texture Atlas for.
Go to "Properties Panel - Render - Texture Atlas" and click the "+"-icon to create a new Texture Atlas.

Select a reasonable image resolution, select "No_Unwrap" and then "ManualUnwrap".

In the UV/Image Editor, go to "Menu - UV - Average Island Scale" (this provides uniform texture spaces for all the objects), then "Menu - UV - Pack Islands".

Move around all UV islands, until satisfied.
Select "FinishManualUnwrap". 
Bake the textures from every object individually to the new Texture Atlas.